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This section describes various tasks which are performed on a periodic basis to keep the codebase up to date with various third-party packages. This includes the versions used for the superbuild, and ensuring that the code will compile against various upstream releases, from the latest stable release to the versions in common use over a range of platforms. It also includes keeping the codebase usable as the toolchains on the supported platforms are updated.

General package maintenance

Keep up to date with all new upstream releases of third-party packages, in particular for security updates. zlib and png are notable here, but this applies to all packages. Check all packages are the current stable version before making a new release. In the case of a security vulnerability, it is possible to release and provide builds with just the vulnerable package updated.

In the simple case of a package which requires no special additional patching, for example png or zlib, updating is as simple as editing packages/<package>/superbuild.cmake:

  • update the source URL
  • update the source hash

For a point release, this is typically sufficient. For a major release, also:

  • check for any changes in the package prerequisites
  • add or update missing prerequisites if required
  • update the prerequisites if required

Regenerating patches

For packages containing patches under packages/<package>/patches, each patch will require individually applying and re-diffing in sequence to regenerate them against the new source release.

  • download and unpack the source release
  • make a copy of the source directory with a .orig extension

For each patch in the order they are listed in the packages/<package>/patches/series file:

  • cd to the source directory
  • apply the patch with patch -p1 < <patchfile>
  • note any rejected hunks and apply these changes by hand as necessary
  • delete any stray patch .orig and .rej files, and also any editor backup files e.g. :file`*~`
  • cd to the parent directory
  • regenerate the diff with diff -urN <source>.orig <source> > <patchfile> and copy it back to the patch directory after checking it
  • delete or rename the <source>.orig directory, and then copy the source directory to <source>.orig; this is to ensure that patches are applied on top of each other to avoid conflicts

This process can be managed with tools like quilt if preferred.

Note that the line ending style used in patch files matters. It must match the type used in the original source files or else it won’t apply. The .gitattributes should help on committing and checking out files, but you do need to make sure you create the diff on the correct operating system; i.e. don’t diff Unix sources on Windows, and double-check the line ending style of the patch matches what was already committed. If this is done incorrectly, the patch will apply only on Unix or only on Windows.

Packages with specific requirements

The following packages require special care when upgrading or maintaining. Please follow the instructions exactly to avoid breakage when upgrading to a new upstream version, and also refer to them when making any other changes.

Toolchain support and standards conformance

Currently the code is built and tested on several platforms, including:

  • FreeBSD with clang++ 3.4
  • Linux with GCC 4.8 to 5.2
  • MacOS X with clang++ (non-standard Mac LLVM/clang++ versions)
  • Windows with VC12 and VC14 (Visual Studio 2013 and 2015)

Testing on a range of version combinations of compilers and platforms is helpful in picking up bugs which would otherwise go undiagnosed until encountered by an end-user. For example, the FreeBSD builds pick up problems which are not noticed on MacOS X by default, though they could still occur in practice (e.g. since MacOS X has a non-standard clang++ and libc++ which have a number of odd quirks). There are also differences between compiler versions e.g. GCC on Linux and clang++ on MacOS, making testing multiple versions useful to pick up portability issues as early as practical. We cannot test every compiler and OS version, along with all the different versions of third-party libraries we depend upon, so we make a best effort to test as wide a range of what is in common use as possible. Inevitably, some issues will remain undiscovered if they are only seen with an untested set of combinations.

Over time, OS releases will reach their end of life, and new replacements will appear. The test matrix will require adjusting to add new platforms and drop old ones. This should be straightforward, but if the platform is new or significantly changed then it may require code changes to correct any exposed portability issue or latent bug which might break the CI builds. It may also require special-casing support for the platform; there are portability headers in ome-common for this purpose, as well as CMake platform checks, which may be updated as required to add support.

Feature testing and compatibility code

Currently, we support and test two separate sets of third-party library versions for each supported platform:

  • the libraries provided by the distribution’s package management system, where applicable (includes homebrew on MacOS X)
  • the libraries provided by the superbuild

The first ensures compatibility of our libraries and headers with the system as a whole; this is necessary to allow use of our libraries with all the libraries provided by the system. The second ensures that the current version of each library is buildable and usable across all the supported platforms, and this allows for the use of current libraries on older systems such as enterprise Linux distributions. This also means we test up to several versions of each library, increasing our test coverage for portability and correctness purposes.

Over time, portability workarounds we have put in place may be dropped. Examples include:

  • dropping functionality checks and workarounds for functionality and behavior differences, e.g. missing filesystem functions and geometry and endian libraries in older Boost releases
  • using the standard implementation of various functions, e.g. std::regex in C++11, std::make_unique() in C++14, filesystem functions in C++17, where the Boost equivalents are currently used; this will reduce our dependency upon Boost over time, once the set of platforms we support all support the functionality we require; note that having the functionality does not make it usable, e.g. GCC has std::regex but it is broken until 5.1 meaning that we need to use boost::regex for the time being; use CMake feature tests to test that each feature is functional as well as present

Such changes should be safe to make with the existing test coverage we have in place.